On molecular homology and common ancestry

For an interesting conversation that I’ve gone and gotten myself into, check out this open thread at Telic Thoughts. (cont’d from here)

There I’m explaining to Krauze, Mung, and others – the evidences for common ancestry in the universally common features of the molecular machinery of the cell, among other things, with passing references to Ciccarelli et al., Knight et al., and this very extensive reference list for research on identifying the root of the Tree of Life supporting the universal common descent and trying to narrow down the identity of the last universal common ancestor (LUCA).

Quite a bit of reading if you’d like to catch up and join in, but it’s worth it. Highlights from the thread are below the fold…
I kind of get Mung’s point that if I’m going to ask for a specific demonstration of the designer, then I should have to physically produce a common ancestor for some major evolutionary event (the LUCA in particular). I acknowledge that point, but he misses mine: that I’m citing a consilience of knowledge that such common ancestry is undeniable. Circumstantial, I suppose, but an extraordinarily large amount of circumstantial evidence, that has no better explanation than common ancestry. So I’ve clarified:

That I have to physically show a common ancestor is over-doing it a bit. If it helps, fine, I’ll take back the claim that you have to physically show me the designer – but you do have to present a line of evidence which demonstrates Special Creation, Divine Intervention, or Assembly of Life de novo, at the exclusion of Descent With Modification.

I’m making the case for cellular and molecular homology of all life to, and descent with modification from, a gram-positive thermophile. How do you chose to respond? (and please, cite actual features of supposed design or failures of descent with modification to explain biological change).